Aflatoxins are mycotoxins considered to be highly toxic and produce adverse effects on human health. These compounds, mainly aflatoxin B₁ (AFB₁), have been classified as human carcinogens, due to its association with the development of hepatocellular carcinoma. In Mexico, the study of aflatoxins has been focused on the evaluation of products of the basic basket, particularly on maize, which is the basis of the Mexican diet. On the other hand, most of these studies have been conducted in urban areas. Indigenous populations may be exposed to a higher risk than urban ones due to the high consumption of tortillas, the harvest and the storage conditions of their food; hence, AFB₁ is frequently found contaminating maize, which is the main food source for Mexicans. There is scarce evidence of exposure in vulnerable populations, such as children. Therefore, the main objective of this research was to conduct a pilot study for the evaluation of exposure to AFB₁ through the AFB₁-lys adduct in 31 serum samples of children from indigenous communities in Mexico. AFB₁-lys was measured by High Pressure Liquid Chromatography with fluorescence detector (HPLC-FLD), with limits of detection and quantification of 3.5 and 4.7 pg/ml, respectively. Results from this pilot study revealed that 13% of children were of short stature, 9.7% presented overweight and 6.5% obesity. 45% of the children presented detectable concentrations of AFB₁-lys adduct, with a median (minimum-maximum) of 5.6 (4.8-6.5) pg of AFB₁-lys adduct/mg of albumin. The AFB₁-lysine exposure biomarker is an important tool for the surveillance of aflatoxins and their effects on health, so, following this intervention, it would be necessary to monitor the exposure of vulnerable populations to aflatoxins, especially in rural areas where foods are more contaminated.